Windows and Linux are two different operating systems. Linux is more efficient and more secure than Windows. Linux is the preferred choice unless you have websites which need a Windows server. Windows Applications which require a Windows server are as following: ASP.NET, MSSQL, MS Acess, and Expression Web. Another difference is that Linux files are case-sensitive while Windows files are not. For example: On a Linux server, index.html and Index.html are different names. On a Windows server, home.html, Index.html, and INDEX.HTML are the same.